In the early years of establishment, the Library was organized into Acquisition Section, Cataloging Section and Reader's Service Section.
Due to service expansion, the former Director Hu, Ou-Lan who took the office in 1990, started a project to reorganize the departments in the Library.
- In 1990, the Stack Management Section was founded.
- In 1992, the System Information Section was established to supervise the daily operation of the Library's automated systems.
- In 1992, periodicals and newspaper collections became the Periodical Section that operated separately from originated Reader's Service Section. The Library organization hence included Acquisition Section, Cataloging Section, Reader's Service Section, Stack Management Section, System Information Section and Periodical Section.
- In 1996, the Reference Services Section became structural subdivision of the Library to provide information retrieval and reference services.
- In 1996, Stack Management Section merged with Reader's Service Section and the Library was reorganized to have Acquisition Section, Cataloging Section, Reader's Service Section, Reference Services Section and Periodical Section.
Due to the rapid growth of electronic resources and increasing needs on digitization of resources, the Library was reorganized to have the following sections effective in February 2008.
- System Information Section: maintains the library's automated systems and develops and implements information security strategies.
- Acquisition and Cataloging Section: selects and acquires materials for inclusion in the collections and maintains records in the library's catalog that provide bibliographic information available to the users.
- Circulation Section: provides loan services and maintains the collection in perfect order on shelves.
- Reference Services Section: assists in using the library resources and services.
- Digital Preservation Section: establishes digitizing project partnership with individuals or organizations of interests and conducts digitization projects.
- Administrative Section: maintains the library building and facilitates for the safety and comfort of the users.
- Branch Libraries: consist of Communication Library, Commerce Library and the Social Sciences Library and mainly provides circulation, reference and library instruction services to affiliated faculty and students.
- Effective February 1, 2013, the Institute of International Relations Library, with core collections of Mainland China's publications, international relationship, economics, military studies and international communist, became the fourth branch library of NCCU and acquisition, stack management and reader's services were all integrated and under the stewardship of the Main Library.